We are conducting the largest meta-analysis of genome-wide association studies of endometriosis to date, involving 21 datasets and more than 60K cases globally. One of the aims is to conduct deep phenotypic analyses of loci in surgically confirmed cases. We have generated one such dataset in-house, involving women who participated in our ENDOX study, who were recruited as they were undergoing laparoscopic surgery for pelvic pain, infertility and sterilization at the John Radcliffe Hospital, Oxford. The participants complete very detailed standardised health questionnaire (endometriosis.org/ephect) on their symptomatology leading to their surgery and medical history of related comorbidities. From this deeply phenotyped resource we have genotyped 200 endometriosis cases using the Illumina Global Screening Array, but no controls. We aim to conduct a GWAS analysis using on these deeply phenotyped endometriosis cases, which will be valuable for phenotypic characterization of GWAS loci from the overall meta-analyses, and hence need a UK female dataset genotyped on an Illumina platform that could be used in the analysis. We are applying to ALSPAC for access to genome-wide genotype call data (Illumina platform) from a set of unrelated women of European ancestry. We assume endometriosis status is unknown and therefore cannot be filtered on. We will merge the genotype data from the ALSPAC controls with our endometriosis cases and use the common set of genotyped SNPs for analyses, including stringent QC (including investigation of potential batch effects and subtle substructure), prephasing and HRC imputation. We will run the association testing as implemented in SNPTEST for case/control analysis. Analyses will be conducted on secure servers at the Wellcome Centre for Human Genetics, where key members of our analytical team are based. The results of the GWAS will be contributed to the International Endometriosis Genomics Consortium (IEGC) GWAS meta-analysis, with of course recognition of ALSPAC’s contributions including co-authorships.